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ds004173-catqc/logs/10070975.out
Felix Hoffstaedter b5c00fc272 add logs
2025-10-23 16:31:13 +02:00

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install(ok): /var/lib/condor/execute/dir_4139128/ds (dataset)
install(ok): /var/lib/condor/execute/dir_4139128/ds/sourcedata/raw (dataset) [Installed subdataset in order to get /var/lib/condor/execute/dir_4139128/ds/sourcedata/raw]
------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is .:/usr/local/MATLAB/MATLAB_Runtime/R2023b/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/R2023b/bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/R2023b/sys/os/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/R2023b/sys/opengl/lib/glnxa64
SPM25, version 25.01.02 (standalone)
MATLAB, version 23.2.0.2859533 (R2023b) Update 10
___ ____ __ __
/ __)( _ \( \/ )
\__ \ )___/ ) ( Statistical Parametric Mapping
(___/(__) (_/\/\_) SPM25 - https://www.fil.ion.ucl.ac.uk/spm/
Item opts: No field(s) named
ngaus
warpreg
bias
acc
redspmres
Item registration: No field(s) named
T1
brainmask
cat12atlas
darteltpm
shootingtpm
regstr
Item atlas: No field(s) named
warped
dartel
------------------------------------------------------------------------
22-Oct-2025 00:38:54 - Running job #1
------------------------------------------------------------------------
22-Oct-2025 00:38:54 - Running 'CAT12: Segmentation'
--------------------------------------------
No commercial use of LPBA40 atlas!
Permission is granted to use this atlas without charge for non-commercial research purposes only:
<a href = "https://www.loni.usc.edu/docs/atlases_methods/Human_Atlas_Methods.pdf">https://www.loni.usc.edu/docs/atlases_methods/Human_Atlas_Methods.pdf</a>
--------------------------------------------
--------------------------------------------
No commercial use of SUIT cerebellar atlas!
Creative Commons Attribution-NonCommercial 3.0 Unported License does not allow commercial use.
--------------------------------------------
Uncompress /var/lib/condor/execute/dir_4139128/ds/sub-598630/sub-598630_acq-headmotion2_T1w.nii
------------------------------------------------------------------------
CAT12.9 r2665: 1/1: ./ds/sub-598630/sub-598630_acq-headmotion2_T1w.n
------------------------------------------------------------------------
SANLM denoising (medium) 52s
Affine preprocessing (APP)
Initialize 6s
Estimate background 6s
Initial correction 6s
Refine background 3s
Final correction 4s
Final scaling 5s
35s
Correct center-of-mass 3s
Affine registration 6s
SPM preprocessing 1 (estimate 1 - TPM registration): Fontconfig error: Cannot load default config file
Fontconfig error: Cannot load default config file
67s
SPM preprocessing 1 (estimate 2): 43s
SPM preprocessing 2 (write)
Write Segmentation 16s
Update Segmentation 13s
Update Skull-Stripping 36s
Update probability maps 7s
72s
Global intensity correction 13s
SANLM denoising after intensity normalization (medium) 16s
Fast Optimized Shooting registration 8s
83s
Local adaptive segmentation (LASstr=0.50)
Prepare maps 3s
Prepare partitions 1s
Prepare segments (LASmod = 1.22) 13s
Estimate local tissue thresholds (WM) 17s
Estimate local tissue thresholds (GM) 20s
Intensity transformation 0s
SANLM denoising after LAS (medium) 26s
82s
ROI segmentation (partitioning)
Atlas -> subject space 7s
Major structures 16s
Ventricle detection 14s
Blood vessel detection 8s
WMH detection (WMHCstr=0.50 > WMHCstr'=0.14) 66s
Manual stroke lesion detection 0s
Closing of deep structures 1s
Side alignment 4s
Final corrections 2s
119s
No enhanced blood vessel correction is required 1s
Amap using initial SPM12 segmentations (MRF filter strength 0.06) 26s
AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
Final cleanup (gcutstr=0.25)
Level 1 cleanup (ROI estimation) 4s
Level 1 cleanup (brain masking) 3s
Level 2 cleanup (CSF correction) 2s
Level 3 cleanup (CSF/WM PVE) 2s
11s
8s
Write result maps 1s
ROI estimation in native space
ROI estimation of 'thalamic_nuclei' atlas 2s
ROI estimation of 'cobra' atlas 6s
ROI estimation of 'neuromorphometrics' atlas 22s
ROI estimation of 'lpba40' atlas 6s
ROI estimation of 'hammers' atlas 16s
ROI estimation of 'thalamus' atlas 1s
ROI estimation of 'suit' atlas 3s
ROI estimation of 'ibsr' atlas 6s
ROI estimation of 'aal3' atlas 9s
ROI estimation of 'mori' atlas 12s
ROI estimation of 'anatomy3' atlas 17s
ROI estimation of 'julichbrain' atlas 22s
ROI estimation of 'Tian_Subcortex_S4_7T' atlas 4s
ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 9s
ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 18s
ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 41s
ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 55s
Write results 56s
251s
Quality check 12s
/var/lib/condor/execute/dir_4139128/ds/sub-598630/report/catreport_sub-598630_acq-headmotion2_T1w.pdf
------------------------------------------------------------------------
CAT preprocessing takes 18 minute(s) and 5 second(s).
Image Quality Rating (IQR): 85.93% (B)
GM volume (GMV): 39.13% (685.38 / 1751.51 ml)
Segmentations are saved in /var/lib/condor/execute/dir_4139128/ds/sub-598630/mri
Reports are saved in /var/lib/condor/execute/dir_4139128/ds/sub-598630/report
Labels are saved in /var/lib/condor/execute/dir_4139128/ds/sub-598630/label
------------------------------------------------------------------------
22-Oct-2025 00:57:01 - Done 'CAT12: Segmentation'
22-Oct-2025 00:57:01 - Done
Bye for now...
get(ok): sourcedata/raw/sub-598630/anat/sub-598630_acq-headmotion2_T1w.nii.gz (file) [from s3-PUBLIC...]
install(ok): code/cat12 (dataset) [Installed subdataset in order to get /var/lib/condor/execute/dir_4139128/ds/code/cat12]
get(ok): code/cat12/cat12.9_r2665.simg (file) [from inm7-storage...]
run(ok): /var/lib/condor/execute/dir_4139128/ds (dataset) [singularity exec -B /var/lib/condor/exec...]
add(ok): sub-598630/label/catROI_sub-598630_acq-headmotion2_T1w.mat (file)
add(ok): sub-598630/label/catROI_sub-598630_acq-headmotion2_T1w.xml (file)
add(ok): sub-598630/mri/it_sub-598630_acq-headmotion2_T1w_affine_reorient.mat (file)
add(ok): sub-598630/mri/it_sub-598630_acq-headmotion2_T1w_rigid_reorient.mat (file)
add(ok): sub-598630/mri/m0wp1sub-598630_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-598630/mri/mwp1sub-598630_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-598630/mri/p0sub-598630_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-598630/mri/t_sub-598630_acq-headmotion2_T1w_affine_reorient.mat (file)
add(ok): sub-598630/mri/t_sub-598630_acq-headmotion2_T1w_rigid_reorient.mat (file)
add(ok): sub-598630/mri/wp0sub-598630_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-598630/report/cat_sub-598630_acq-headmotion2_T1w.mat (file)
add(ok): sub-598630/report/cat_sub-598630_acq-headmotion2_T1w.xml (file)
add(ok): sub-598630/report/catlog_sub-598630_acq-headmotion2_T1w.txt (file)
add(ok): sub-598630/report/catreport_sub-598630_acq-headmotion2_T1w.pdf (file)
save(ok): . (dataset)
action summary:
add (ok: 14)
get (notneeded: 2, ok: 2)
install (ok: 1)
run (ok: 1)
save (ok: 1)
------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is .:/usr/local/MATLAB/MATLAB_Runtime/R2023b/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/R2023b/bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/R2023b/sys/os/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/R2023b/sys/opengl/lib/glnxa64
SPM25, version 25.01.02 (standalone)
MATLAB, version 23.2.0.2859533 (R2023b) Update 10
___ ____ __ __
/ __)( _ \( \/ )
\__ \ )___/ ) ( Statistical Parametric Mapping
(___/(__) (_/\/\_) SPM25 - https://www.fil.ion.ucl.ac.uk/spm/
Item opts: No field(s) named
ngaus
warpreg
bias
acc
redspmres
Item registration: No field(s) named
T1
brainmask
cat12atlas
darteltpm
shootingtpm
regstr
Item atlas: No field(s) named
warped
dartel
------------------------------------------------------------------------
22-Oct-2025 00:57:34 - Running job #1
------------------------------------------------------------------------
22-Oct-2025 00:57:34 - Running 'CAT12: Segmentation'
--------------------------------------------
No commercial use of LPBA40 atlas!
Permission is granted to use this atlas without charge for non-commercial research purposes only:
<a href = "https://www.loni.usc.edu/docs/atlases_methods/Human_Atlas_Methods.pdf">https://www.loni.usc.edu/docs/atlases_methods/Human_Atlas_Methods.pdf</a>
--------------------------------------------
--------------------------------------------
No commercial use of SUIT cerebellar atlas!
Creative Commons Attribution-NonCommercial 3.0 Unported License does not allow commercial use.
--------------------------------------------
Uncompress /var/lib/condor/execute/dir_4139128/ds/sub-598630/sub-598630_acq-standard_T1w.nii
------------------------------------------------------------------------
CAT12.9 r2665: 1/1: ./ds/sub-598630/sub-598630_acq-standard_T1w.n
------------------------------------------------------------------------
SANLM denoising (medium) 51s
Affine preprocessing (APP)
Initialize 6s
Estimate background 6s
Initial correction 6s
Refine background 3s
Final correction 4s
Final scaling 5s
35s
Correct center-of-mass 3s
Affine registration 6s
SPM preprocessing 1 (estimate 1 - TPM registration): Fontconfig error: Cannot load default config file
Fontconfig error: Cannot load default config file
64s
SPM preprocessing 1 (estimate 2): 43s
SPM preprocessing 2 (write)
Write Segmentation 16s
Update Segmentation 13s
Update Skull-Stripping 37s
Update probability maps 7s
73s
Global intensity correction 13s
SANLM denoising after intensity normalization (medium) 16s
Fast Optimized Shooting registration 9s
84s
Local adaptive segmentation (LASstr=0.50)
Prepare maps 3s
Prepare partitions 1s
Prepare segments (LASmod = 1.07) 13s
Estimate local tissue thresholds (WM) 17s
Estimate local tissue thresholds (GM) 20s
Intensity transformation 0s
SANLM denoising after LAS (medium) 25s
83s
ROI segmentation (partitioning)
Atlas -> subject space 7s
Major structures 16s
Ventricle detection 15s
Blood vessel detection 9s
WMH detection (WMHCstr=0.50 > WMHCstr'=0.14) 76s
Manual stroke lesion detection 0s
Closing of deep structures 1s
Side alignment 4s
Final corrections 2s
130s
No enhanced blood vessel correction is required 1s
Amap using initial SPM12 segmentations (MRF filter strength 0.06) 25s
AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.04]
Final cleanup (gcutstr=0.25)
Level 1 cleanup (ROI estimation) 4s
Level 1 cleanup (brain masking) 3s
Level 2 cleanup (CSF correction) 2s
Level 3 cleanup (CSF/WM PVE) 2s
11s
5s
Write result maps 1s
ROI estimation in native space
ROI estimation of 'thalamic_nuclei' atlas 2s
ROI estimation of 'cobra' atlas 6s
ROI estimation of 'neuromorphometrics' atlas 22s
ROI estimation of 'lpba40' atlas 6s
ROI estimation of 'hammers' atlas 15s
ROI estimation of 'thalamus' atlas 1s
ROI estimation of 'suit' atlas 3s
ROI estimation of 'ibsr' atlas 5s
ROI estimation of 'aal3' atlas 9s
ROI estimation of 'mori' atlas 11s
ROI estimation of 'anatomy3' atlas 16s
ROI estimation of 'julichbrain' atlas 21s
ROI estimation of 'Tian_Subcortex_S4_7T' atlas 3s
ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 9s
ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 17s
ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 39s
ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 53s
Write results 54s
242s
Quality check 12s
/var/lib/condor/execute/dir_4139128/ds/sub-598630/report/catreport_sub-598630_acq-standard_T1w.pdf
------------------------------------------------------------------------
CAT preprocessing takes 17 minute(s) and 59 second(s).
Image Quality Rating (IQR): 87.89% (B+)
GM volume (GMV): 40.03% (704.53 / 1760.21 ml)
Segmentations are saved in /var/lib/condor/execute/dir_4139128/ds/sub-598630/mri
Reports are saved in /var/lib/condor/execute/dir_4139128/ds/sub-598630/report
Labels are saved in /var/lib/condor/execute/dir_4139128/ds/sub-598630/label
------------------------------------------------------------------------
22-Oct-2025 01:15:35 - Done 'CAT12: Segmentation'
22-Oct-2025 01:15:35 - Done
Bye for now...
get(ok): sourcedata/raw/sub-598630/anat/sub-598630_acq-standard_T1w.nii.gz (file) [from s3-PUBLIC...]
unlock(ok): sub-598630/label/catROI_sub-598630_acq-headmotion2_T1w.mat (file)
unlock(ok): sub-598630/mri/it_sub-598630_acq-headmotion2_T1w_affine_reorient.mat (file)
unlock(ok): sub-598630/mri/it_sub-598630_acq-headmotion2_T1w_rigid_reorient.mat (file)
unlock(ok): sub-598630/mri/m0wp1sub-598630_acq-headmotion2_T1w.nii.gz (file)
unlock(ok): sub-598630/mri/mwp1sub-598630_acq-headmotion2_T1w.nii.gz (file)
unlock(ok): sub-598630/mri/p0sub-598630_acq-headmotion2_T1w.nii.gz (file)
unlock(ok): sub-598630/mri/t_sub-598630_acq-headmotion2_T1w_affine_reorient.mat (file)
unlock(ok): sub-598630/mri/t_sub-598630_acq-headmotion2_T1w_rigid_reorient.mat (file)
unlock(ok): sub-598630/mri/wp0sub-598630_acq-headmotion2_T1w.nii.gz (file)
unlock(ok): sub-598630/report/cat_sub-598630_acq-headmotion2_T1w.mat (file)
unlock(ok): sub-598630/report/catreport_sub-598630_acq-headmotion2_T1w.pdf (file)
run(ok): /var/lib/condor/execute/dir_4139128/ds (dataset) [singularity exec -B /var/lib/condor/exec...]
add(ok): sub-598630/label/catROI_sub-598630_acq-standard_T1w.mat (file)
add(ok): sub-598630/label/catROI_sub-598630_acq-standard_T1w.xml (file)
add(ok): sub-598630/mri/it_sub-598630_acq-standard_T1w_affine_reorient.mat (file)
add(ok): sub-598630/mri/it_sub-598630_acq-standard_T1w_rigid_reorient.mat (file)
add(ok): sub-598630/mri/m0wp1sub-598630_acq-standard_T1w.nii.gz (file)
add(ok): sub-598630/mri/mwp1sub-598630_acq-standard_T1w.nii.gz (file)
add(ok): sub-598630/mri/p0sub-598630_acq-standard_T1w.nii.gz (file)
add(ok): sub-598630/mri/t_sub-598630_acq-standard_T1w_affine_reorient.mat (file)
add(ok): sub-598630/mri/t_sub-598630_acq-standard_T1w_rigid_reorient.mat (file)
add(ok): sub-598630/mri/wp0sub-598630_acq-standard_T1w.nii.gz (file)
add(ok): sub-598630/report/cat_sub-598630_acq-standard_T1w.mat (file)
add(ok): sub-598630/report/cat_sub-598630_acq-standard_T1w.xml (file)
add(ok): sub-598630/report/catlog_sub-598630_acq-standard_T1w.txt (file)
add(ok): sub-598630/report/catreport_sub-598630_acq-standard_T1w.pdf (file)
add(ok): sub-598630/label/catROI_sub-598630_acq-headmotion2_T1w.mat (file)
add(ok): sub-598630/mri/it_sub-598630_acq-headmotion2_T1w_affine_reorient.mat (file)
add(ok): sub-598630/mri/it_sub-598630_acq-headmotion2_T1w_rigid_reorient.mat (file)
add(ok): sub-598630/mri/m0wp1sub-598630_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-598630/mri/mwp1sub-598630_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-598630/mri/p0sub-598630_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-598630/mri/t_sub-598630_acq-headmotion2_T1w_affine_reorient.mat (file)
add(ok): sub-598630/mri/t_sub-598630_acq-headmotion2_T1w_rigid_reorient.mat (file)
add(ok): sub-598630/mri/wp0sub-598630_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-598630/report/cat_sub-598630_acq-headmotion2_T1w.mat (file)
add(ok): sub-598630/report/catreport_sub-598630_acq-headmotion2_T1w.pdf (file)
save(ok): . (dataset)
action summary:
add (ok: 25)
get (notneeded: 4, ok: 1)
run (ok: 1)
save (ok: 1)
unlock (ok: 11)
copy(ok): sub-598630/label/catROI_sub-598630_acq-headmotion2_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-598630/label/catROI_sub-598630_acq-standard_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-598630/mri/it_sub-598630_acq-headmotion2_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-598630/mri/it_sub-598630_acq-headmotion2_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-598630/mri/it_sub-598630_acq-standard_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-598630/mri/it_sub-598630_acq-standard_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-598630/mri/m0wp1sub-598630_acq-headmotion2_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-598630/mri/m0wp1sub-598630_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-598630/mri/mwp1sub-598630_acq-headmotion2_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-598630/mri/mwp1sub-598630_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-598630/mri/p0sub-598630_acq-headmotion2_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-598630/mri/p0sub-598630_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-598630/mri/t_sub-598630_acq-headmotion2_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-598630/mri/t_sub-598630_acq-headmotion2_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-598630/mri/t_sub-598630_acq-standard_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-598630/mri/t_sub-598630_acq-standard_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-598630/mri/wp0sub-598630_acq-headmotion2_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-598630/mri/wp0sub-598630_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-598630/report/cat_sub-598630_acq-headmotion2_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-598630/report/cat_sub-598630_acq-standard_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-598630/report/catreport_sub-598630_acq-headmotion2_T1w.pdf (file) [to catqc_out-storage...]
copy(ok): sub-598630/report/catreport_sub-598630_acq-standard_T1w.pdf (file) [to catqc_out-storage...]
action summary:
copy (ok: 22)
flock: getting lock took 0.000697 seconds
flock: executing git
SUCCESS
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